Prime Minister Benjamin Netanyahu said that Israel is ready to resume fighting if Hamas fails to release more hostages by 12pm on Saturday.
Munir al-Bursh, director general of the ministry, said at least 92 Palestinians have been killed and more than 800 wounded by Israeli fire since the fragile ceasefire took hold last month.
Hamas has stunned the world by announcing it would halt the exchange of hostages, a accusing Israel of keeping aid from reaching northern Gaza.
Gaza's health ministry said a 44-year-old man was killed in an Israeli strike near the southern city of Rafah on Wednesday.
And he branded US President Donald Trump a "fool" for issuing a similar ultimatum to Hamas, which was followed up by Israeli Prime Minister Benjamin Netanyahu.